Evolution and diversity of secretome genes in the apicomplexan parasite Theileria annulata

<b>BACKGROUND</b>: Little is known about how apicomplexan parasites have evolved to infect different host species and cell types. Theileria annulata and Theileria parva invade and transform bovine leukocytes but each species favours a different host cell lineage. Parasite-encoded proteins secreted from the intracellular macroschizont stage within the leukocyte represent a critical interface between host and pathogen systems. Genome sequencing has revealed that several Theileria-specific gene families encoding secreted proteins are positively selected at the inter-species level, indicating diversification between the species. We extend this analysis to the intra-species level, focusing on allelic diversity of two major secretome families. These families represent a well-characterised group of genes implicated in control of the host cell phenotype and a gene family of unknown function. To gain further insight into their evolution and function, this study investigates whether representative genes of these two families are diversifying or constrained within the T. annulata population. <b>RESULTS</b>: Strong evidence is provided that the sub-telomerically encoded SVSP family and the host-nucleus targeted TashAT family have evolved under contrasting pressures within natural T. annulata populations. SVSP genes were found to possess atypical codon usage and be evolving neutrally, with high levels of nucleotide substitutions and multiple indels. No evidence of geographical sub-structuring of allelic sequences was found. In contrast, TashAT family genes, implicated in control of host cell gene expression, are strongly conserved at the protein level and geographically sub-structured allelic sequences were identified among Tunisian and Turkish isolates. Although different copy numbers of DNA binding motifs were identified in alleles of TashAT proteins, motif periodicity was strongly maintained, implying conserved functional activity of these sites. <b>CONCLUSIONS</b>: This analysis provides evidence that two distinct secretome genes families have evolved under contrasting selective pressures. The data supports current hypotheses regarding the biological role of TashAT family proteins in the management of host cell phenotype that may have evolved to allow adaptation of T. annulata to a specific host cell lineage. We provide new evidence of extensive allelic diversity in representative members of the enigmatic SVSP gene family, which supports a putative role for the encoded products in subversion of the host immune response

Fluxoid formation: size effects and non-equilibrium universality

Simple causal arguments put forward by Kibble and Zurek suggest that the scaling behaviour of condensed matter at continuous transitions is related to the familiar universality classes of the systems at quasi-equilibrium. Although proposed 25 years ago or more, it is only in the last few years that it has been possible to devise experiments from which scaling exponents can be determined and in which this scenario can be tested. In previous work, an unusually high Kibble-Zurek scaling exponent was reported for spontaneous fluxoid production in a single isolated superconducting Nb loop, albeit with low density. Using analytic approximations backed up by Langevin simulations, we argue that densities as small as these are too low to be attributable to scaling, and are conditioned by the small size of the loop. We also reflect on the physical differences between slow quenches and small rings, and derive some criteria for these differences, noting that recent work on slow quenches does not adequately explain the anomalous behaviour seen here.Comment: 7 pages, 4 figures, presentation given at CMMP 201

Defect formation in superconducting rings: external fields and finite-size effects

Consistent with the predictions of Kibble and Zurek, scaling behaviour has been seen in the production of fluxoids during temperature quenches of superconducting rings. However, deviations from the canonical behaviour arise because of finite-size effects and stray external fields. Technical developments, including laser heating and the use of long Josephson tunnel junctions, have improved the quality of data that can be obtained. With new experiments in mind we perform large-scale 3D simulations of quenches of small, thin rings of various geometries with fully dynamical electromagnetic fields, at nonzero externally applied magnetic flux. We find that the outcomes are, in practice, indistinguishable from those of much simpler Gaussian analytical approximations in which the rings are treated as one-dimensional systems and the magnetic field fluctuation-free.Comment: 10 pages, 3 figures, presentation at QFS2012, to appear in JLT

Bridge Grafting

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Metallic liquid hydrogen and likely Al2O3 metallic glass

Dynamic compression has been used to synthesize liquid metallic hydrogen at 140 GPa (1.4 million bar) and experimental data and theory predict Al2O3 might be a metallic glass at ~300 GPa. The mechanism of metallization in both cases is probably a Mott-like transition. The strength of sapphire causes shock dissipation to be split differently in the strong solid and soft fluid. Once the 4.5-eV H-H and Al-O bonds are broken at sufficiently high pressures in liquid H2 and in sapphire (single-crystal Al2O3), electrons are delocalized, which leads to formation of energy bands in fluid H and probably in amorphous Al2O3. The high strength of sapphire causes shock dissipation to be absorbed primarily in entropy up to ~400 GPa, which also causes the 300-K isotherm and Hugoniot to be virtually coincident in this pressure range. Above ~400 GPa shock dissipation must go primarily into temperature, which is observed experimentally as a rapid increase in shock pressure above ~400 GPa. The metallization of glassy Al2O3, if verified, is expected to be general in strong oxide insulators. Implications for Super Earths are discussed.Comment: 8 pages, 5 figures, 14th Liquid and Amorphous Metals Conference, Rome 201